GEO DataSets

(Submitter supplied) The TyrR transcription factor controls the expression of genes for the uptake and biosynthesis of aromatic amino acids in Escherichia coli. In the plant-associated and clinically significant proteobacterium Enterobacter ludwigii UW5, the TyrR orthologue was previously shown to regulate genes that encode enzymes for synthesis of the plant hormone indole-3-acetic acid and gluconeogenesis, indicating a broader function for the transcription factor. more...

Organism:

Enterobacter ludwigii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29272

8 Samples

Download data: TXT, XLSX

(Submitter supplied) We show for soil bacterium Enterobacter soli LF7 (synonym Enterobacter asburiae LF7a) that possession of a iac (indole 3-acetic acid catabolic) gene cluster is causatively linked to the ability to utilize the plant hormone indole 3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. more...

Organism:

Enterobacter soli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24961

12 Samples

Download data: TXT

(Submitter supplied) Haemophilus ducreyi 35000HPcpxRpML125 which over-expresses CpxR in a CpxR deletion background, was compared to it vector alone counterpart (35000HPcpxRpLS88) in hopes to elucidate members of the CpxRA regulon.

Organism:

[Haemophilus] ducreyi; [Haemophilus] ducreyi 35000HP

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) Comparative analysis of the global gene expression of a Haemophilus ducreyi 35000HP cpxA deletion mutant relative to the wild type strain

Organism:

[Haemophilus] ducreyi 35000HP; [Haemophilus] ducreyi

Type:

Expression profiling by array

Platform:

GPL7741

6 Samples

Download data: GPR

(Submitter supplied) Pathogenicity islands and plasmids encode genes for pathogenesis of various Escherichia coli pathotypes.Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here we dissected aregulatory network directed by the conserved iron homeostasis regulator, Ferric Uptake Regulator (Fur), inuropathogenic E. more...

Organism:

Escherichia coli CFT073

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18955

19 Samples

Download data: TXT, WIG

(Submitter supplied) To ensure faithful translation of the genetic code, some aminoacyl-tRNA synthetases have a quality control (QC) mechanism that allows them to remove similarly shaped, non-protein amino acids (NPAs) from a mischarged tRNA. In E. coli, the QC function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to the toxic NPA, meta-Tyrosine (m-Tyr).  Here, we sought to understand the mechanism of m-Tyr toxicity. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

12 Samples

Download data: TXT, XLSX

(Submitter supplied) We report 6 genes that were found to be regulated by SoxR in stationary phase when the bacteria produce the antibiotic actinorhodin. Five of these genes are previously confirmed SoxR targets; the sixth is a novel SoxR-target.

Organism:

Streptomyces coelicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17012

6 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) In this study wild-type, fur mutant, and complemented fur mutant strains of the human pathogen Neisseria gonorrhoeae F62 were grown under high (100 uM iron) or low (100 uM desferal) iron conditions to identify genes whose expression was regulated by iron and/or Fur

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20721

10 Samples

Download data: TXT

(Submitter supplied) Citrobacter rodentium is a murine pathogen used to model the intestinal infection caused by Enteropathogenic and Enterohemorrhagic Escherichia coli (EPEC and EHEC), two diarrheal pathogens responsible for morbidity and mortality in developing and developed countries, respectively. During infection, these bacteria must sense and adapt to the gut environment of the host. In order to adapt to changing environmental cues and modulate expression of specific genes, bacteria can use two-component signal transduction systems (TCS). more...

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL25012

12 Samples

Download data: TXT

(Submitter supplied) We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

12 Samples

Download data: GPR

(Submitter supplied) Shewanella oneidensis MR-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent. Knowledge of the molecular components and regulatory mechanisms dictating cellular responses to heavy metal stress, however, remains incomplete. In a previous work, the S. oneidensis so2426 gene, annotated as a DNA-binding response regulator, was demonstrated to be specifically responsive at both the transcript and protein levels to acute chromate [Cr(VI)] challenge. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL7055

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL17024 GPL15010 GPL8708

24 Samples

Download data: PAIR, TXT, WIG

(Submitter supplied) As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we mapped the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

9 Samples

Download data: WIG

(Submitter supplied) As descirbed in the manuscript The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons we performed a control ChIP-chip experiment in an E. coli strain lacking the transcription factor Fur to identify regions Fur-independent enrichment.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8708

1 Sample

Download data: PAIR, TXT

(Submitter supplied) As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we profiled the gene expression of E. coli K12 during aerobic or anaerobic growth and in the presence or absence of the transcription factor Fur and/or the small RNA RyhB.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by genome tiling array

Platform:

GPL8708

14 Samples

Download data: PAIR, TXT